Calibration Data Quality Assessment

IRT Item Response Validation Report

Published

November 10, 2025

Executive Summary

This report provides a comprehensive quality assessment of the IRT calibration dataset, which combines data from 6 studies (NE20, NE22, NE25, NSCH21, NSCH22, USA24) for psychometric modeling.

Data Quality Flags Detected

The validation system detected 3 types of data quality issues:

Category Mismatch: Observed response categories differ from codebook expectations
- Invalid values: Response values not defined in codebook (e.g., value=9 when only {0,1,2} expected)
- Fewer categories: Missing response categories (ceiling/floor effects)
Negative Age-Response Correlation: Items where older children score lower than younger children (developmentally unexpected). Only checked for Kidsights Measurement Tool items; GSED-PF psychosocial items are excluded as they are not developmental.
Non-Sequential Response Values: Response values with gaps (e.g., {0,1,9} instead of {0,1,2}), suggesting undocumented missing codes

Overall Dataset Summary

Flag Summary Statistics

Flag Distribution by Type

Detailed Flag Report

This section provides a comprehensive, filterable table of all detected quality flags.

Interpretation Guide

ERROR flags (red): Require immediate attention - invalid data values detected
WARNING flags (yellow): Noteworthy patterns that may affect modeling
Instruments (color-coded):
- Kidsights Measurement Tool - Developmental items (checked for age correlation)
- GSED-PF - Psychosocial items (excluded from age checks)
Use column filters to focus on specific studies, flag types, or severities
Click “CSV” or “Excel” buttons to export data for further analysis

Item Explorer: Top Flagged Items

This section shows age-response relationships for the most frequently flagged items.

Interactive Version

For a fully interactive item explorer with dropdown selection, run this report as a Shiny app:

library(quarto)
quarto::quarto_preview("docs/irt_scoring/calibration_quality_report.qmd")

This static version shows the top 10 flagged items for quick review.

#| label: plot-all-top-items #| results: asis

for (item in top_items) { cat(sprintf(“## %s”, item))

# Get flags for this item item_flags <- quality_flags %>% filter(item_id == item) %>% select(Study = study, Flag Type = flag_type, Severity = flag_severity, Description = description)

cat(“Flags for this item:”) print(knitr::kable(item_flags, format = “markdown”)) cat(“”)

# Plot age-response relationship p <- plot_item_age_response(item, calibration_data) if (!is.null(p)) { print(p) } else { cat(“No data available for plotting”) }

cat(“—”) }

About This Report

Data Source: calibration_dataset_2020_2025 table (harmonized lex_equate names)
Validation Function: scripts/irt_scoring/validate_calibration_quality.R
Generated: 2025-11-10 10:46:23.586172
Studies: NE20 (n=37,546), NE22 (n=2,431), NE25 (n=3,507), NSCH21 (n=1,000 sampled), NSCH22 (n=1,000 sampled), USA24 (n=1,600)

For questions or to report data quality concerns, contact the Calibration Pipeline Team.

--- title: "Calibration Data Quality Assessment" subtitle: "IRT Item Response Validation Report" date: today format: html: page-layout: full code-fold: true code-tools: true toc: true toc-depth: 3 toc-location: left theme: cosmo embed-resources: true self-contained: true execute: warning: false message: false echo: false --- ```{r setup} #| label: setup #| include: false # Load required packages library(duckdb) library(DBI) library(dplyr) library(tidyr) library(ggplot2) library(plotly) library(DT) library(jsonlite) library(mgcv) library(scales) # Set ggplot theme theme_set(theme_minimal(base_size = 12)) # Define color palette for 6 studies study_colors <- c( "NE20" = "#1f77b4", # Blue "NE22" = "#ff7f0e", # Orange "NE25" = "#2ca02c", # Green "NSCH21" = "#d62728", # Red "NSCH22" = "#9467bd", # Purple "USA24" = "#8c564b" # Brown ) ``` # Executive Summary This report provides a comprehensive quality assessment of the IRT calibration dataset, which combines data from 6 studies (NE20, NE22, NE25, NSCH21, NSCH22, USA24) for psychometric modeling. ## Data Quality Flags Detected The validation system detected **3 types of data quality issues**: 1. **Category Mismatch**: Observed response categories differ from codebook expectations - **Invalid values**: Response values not defined in codebook (e.g., value=9 when only {0,1,2} expected) - **Fewer categories**: Missing response categories (ceiling/floor effects) 2. **Negative Age-Response Correlation**: Items where older children score lower than younger children (developmentally unexpected). **Only checked for Kidsights Measurement Tool items; GSED-PF psychosocial items are excluded as they are not developmental.** 3. **Non-Sequential Response Values**: Response values with gaps (e.g., {0,1,9} instead of {0,1,2}), suggesting undocumented missing codes --- ```{r load_data} #| label: load-data # Load calibration data conn <- dbConnect(duckdb(), "../../data/duckdb/kidsights_local.duckdb", read_only = TRUE) calibration_data <- dbGetQuery(conn, " SELECT * FROM calibration_dataset_2020_2025_restructured ") dbDisconnect(conn) # Load quality flags quality_flags <- read.csv("quality_flags.csv", stringsAsFactors = FALSE) # Load codebook codebook <- fromJSON("../../codebook/data/codebook.json", simplifyVector = FALSE) # Extract instrument mapping from codebook instrument_mapping <- data.frame( item_id = character(), instrument = character(), stringsAsFactors = FALSE ) for (item_id in names(codebook$items)) { item <- codebook$items[[item_id]] if (!is.null(item$lexicons$equate) && !is.null(item$instruments)) { equate_name <- item$lexicons$equate instruments <- unlist(item$instruments) # Create one row per instrument for (inst in instruments) { instrument_mapping <- rbind(instrument_mapping, data.frame( item_id = equate_name, instrument = inst, stringsAsFactors = FALSE )) } } } # Add instrument column to quality flags quality_flags <- quality_flags %>% left_join(instrument_mapping, by = "item_id") # Extract item columns metadata_cols <- c("study_num", "id", "years", "study") item_cols <- setdiff(names(calibration_data), metadata_cols) ``` ## Overall Dataset Summary ```{r summary_table} #| label: summary-table summary_df <- calibration_data %>% group_by(study) %>% summarise( Records = n(), `Age Range` = sprintf("%.1f - %.1f years", min(years, na.rm=TRUE), max(years, na.rm=TRUE)), `Mean Age` = sprintf("%.2f years", mean(years, na.rm=TRUE)), .groups = "drop" ) # Add total row total_row <- data.frame( study = "**TOTAL**", Records = sum(summary_df$Records), `Age Range` = sprintf("%.1f - %.1f years", min(calibration_data$years, na.rm=TRUE), max(calibration_data$years, na.rm=TRUE)), `Mean Age` = sprintf("%.2f years", mean(calibration_data$years, na.rm=TRUE)), check.names = FALSE ) summary_df <- rbind(summary_df, total_row) datatable( summary_df, options = list( pageLength = 10, dom = 't', ordering = FALSE ), rownames = FALSE, escape = FALSE, caption = "Table 1: Calibration Dataset Summary by Study" ) ``` --- ## Flag Summary Statistics ```{r flag_summary} #| label: flag-summary flag_summary <- quality_flags %>% group_by(flag_type, flag_severity) %>% summarise( Count = n(), `Unique Items` = n_distinct(item_id), `Studies Affected` = n_distinct(study), .groups = "drop" ) %>% arrange(desc(Count)) datatable( flag_summary, options = list( pageLength = 10, dom = 't', order = list(list(2, 'desc')) ), rownames = FALSE, caption = "Table 2: Quality Flags by Type and Severity" ) %>% formatStyle( 'flag_severity', backgroundColor = styleEqual(c('ERROR', 'WARNING'), c('#ffcccc', '#fff3cd')) ) ``` --- ## Flag Distribution by Type ```{r flag_barchart} #| label: flag-barchart #| fig-width: 10 #| fig-height: 5 flag_counts <- quality_flags %>% count(flag_type, flag_severity) %>% mutate( flag_type_label = case_when( flag_type == "CATEGORY_MISMATCH_INVALID" ~ "Invalid Values", flag_type == "CATEGORY_MISMATCH_FEWER" ~ "Fewer Categories", flag_type == "NEGATIVE_CORRELATION" ~ "Negative Correlation", flag_type == "NON_SEQUENTIAL" ~ "Non-Sequential Values", TRUE ~ flag_type ) ) p <- ggplot(flag_counts, aes(x = reorder(flag_type_label, -n), y = n, fill = flag_severity)) + geom_col() + geom_text(aes(label = n), position = position_stack(vjust = 0.5), color = "white", size = 5, fontface = "bold") + scale_fill_manual(values = c("ERROR" = "#d9534f", "WARNING" = "#f0ad4e")) + labs( title = "Quality Flags by Type", subtitle = sprintf("Total: %d flags across %d items and %d studies", nrow(quality_flags), n_distinct(quality_flags$item_id), n_distinct(quality_flags$study)), x = NULL, y = "Number of Flags", fill = "Severity" ) + theme( axis.text.x = element_text(angle = 15, hjust = 1), legend.position = "top", plot.title = element_text(face = "bold", size = 16), plot.subtitle = element_text(size = 12) ) ggplotly(p, tooltip = c("x", "y", "fill")) %>% layout(hovermode = "x unified") ``` --- # Detailed Flag Report This section provides a comprehensive, filterable table of all detected quality flags. ```{r detailed_flags} #| label: detailed-flags-table # Prepare detailed flags table detailed_flags <- quality_flags %>% select( Item = item_id, Study = study, Instrument = instrument, `Flag Type` = flag_type, Severity = flag_severity, `Observed Categories` = observed_categories, `Expected Categories` = expected_categories, `Correlation (r)` = correlation_value, `N Responses` = n_responses, `% Missing` = pct_missing, Description = description ) %>% mutate( `% Missing` = round(`% Missing`, 1), `Correlation (r)` = round(`Correlation (r)`, 3) ) datatable( detailed_flags, filter = 'top', extensions = 'Buttons', options = list( pageLength = 25, dom = 'Bfrtip', buttons = c('copy', 'csv', 'excel'), scrollX = TRUE, order = list(list(3, 'asc'), list(1, 'asc')) ), rownames = FALSE, caption = "Table 3: Detailed Quality Flags (Filterable and Exportable)" ) %>% formatStyle( 'Severity', backgroundColor = styleEqual(c('ERROR', 'WARNING'), c('#ffcccc', '#fff3cd')), fontWeight = 'bold' ) %>% formatStyle( 'Instrument', backgroundColor = styleEqual( c('Kidsights Measurement Tool', 'GSED-PF'), c('#d4e6f1', '#fdebd0') # Light blue for Kidsights, light orange for GSED-PF ), fontWeight = 'bold', fontSize = '11px' ) %>% formatStyle( 'Item', fontFamily = 'monospace' ) %>% formatStyle( '% Missing', background = styleColorBar(range(detailed_flags$`% Missing`, na.rm = TRUE), '#e6f2ff'), backgroundSize = '100% 90%', backgroundRepeat = 'no-repeat', backgroundPosition = 'center' ) ``` ::: {.callout-tip} ## Interpretation Guide - **ERROR flags** (red): Require immediate attention - invalid data values detected - **WARNING flags** (yellow): Noteworthy patterns that may affect modeling - **Instruments** (color-coded): - Kidsights Measurement Tool - Developmental items (checked for age correlation) - GSED-PF - Psychosocial items (excluded from age checks) - Use column filters to focus on specific studies, flag types, or severities - Click "CSV" or "Excel" buttons to export data for further analysis ::: --- # Item Explorer: Top Flagged Items This section shows age-response relationships for the most frequently flagged items. ::: {.callout-note} ## Interactive Version For a fully interactive item explorer with dropdown selection, run this report as a Shiny app: ```r library(quarto) quarto::quarto_preview("docs/irt_scoring/calibration_quality_report.qmd") ``` This static version shows the top 10 flagged items for quick review. ::: ```{r top_flagged_items} #| label: top-flagged-items # Get top 10 flagged items top_items <- quality_flags %>% group_by(item_id) %>% summarise( flag_count = n(), studies_affected = paste(unique(study), collapse = ", "), .groups = "drop" ) %>% arrange(desc(flag_count)) %>% slice(1:10) %>% pull(item_id) ``` ```{r plot_item_function} #| label: plot-item-function # Function to create age-response plot for an item plot_item_age_response <- function(item_name, data) { # Filter data plot_data <- data %>% select(study, years, response = !!item_name) %>% filter(!is.na(response)) if (nrow(plot_data) == 0) { return(NULL) } # Determine item type unique_vals <- sort(unique(plot_data$response)) is_binary <- all(unique_vals %in% c(0, 1)) # Fit models per study study_predictions <- list() for (study_name in unique(plot_data$study)) { study_data <- plot_data %>% filter(study == study_name) if (nrow(study_data) < 10) next age_grid <- data.frame(years = seq(min(study_data$years), max(study_data$years), length.out = 100)) tryCatch({ if (is_binary) { model <- glm(response ~ years, data = study_data, family = binomial()) predictions <- predict(model, newdata = age_grid, type = "response") } else { model <- mgcv::gam(response ~ s(years, k = 4), data = study_data) predictions <- predict(model, newdata = age_grid, type = "response") } study_predictions[[study_name]] <- data.frame( study = study_name, years = age_grid$years, predicted = predictions ) }, error = function(e) { NULL }) } # Combine predictions all_predictions <- if (length(study_predictions) > 0) bind_rows(study_predictions) else NULL # Create plot p <- ggplot() + geom_jitter( data = plot_data, aes(x = years, y = response, color = study, text = sprintf("Study: %s Age: %.2f Response: %d", study, years, response)), alpha = 0.3, width = 0.05, height = 0.05, size = 1.5 ) if (!is.null(all_predictions)) { p <- p + geom_line( data = all_predictions, aes(x = years, y = predicted, color = study), size = 1.2 ) } p <- p + scale_color_manual(values = study_colors) + labs( title = sprintf("Item: %s", item_name), subtitle = sprintf("Model: %s | N = %d", ifelse(is_binary, "Logistic Regression", "GAM (k=4)"), nrow(plot_data)), x = "Child Age (years)", y = "Item Response", color = "Study" ) + theme( legend.position = "right", plot.title = element_text(face = "bold", size = 12), plot.subtitle = element_text(size = 10) ) ggplotly(p, tooltip = "text") %>% layout(hovermode = "closest") } ``` ```{r plot_all_top_items} #| label: plot-all-top-items #| results: asis for (item in top_items) { cat(sprintf("\n\n## %s\n\n", item)) # Get flags for this item item_flags <- quality_flags %>% filter(item_id == item) %>% select(Study = study, `Flag Type` = flag_type, Severity = flag_severity, Description = description) cat("**Flags for this item:**\n\n") print(knitr::kable(item_flags, format = "markdown")) cat("\n\n") # Plot age-response relationship p <- plot_item_age_response(item, calibration_data) if (!is.null(p)) { print(p) } else { cat("*No data available for plotting*\n\n") } cat("\n\n---\n\n") } --- ::: {.callout-note} ## About This Report - **Data Source:** `calibration_dataset_2020_2025` table (harmonized lex_equate names) - **Validation Function:** `scripts/irt_scoring/validate_calibration_quality.R` - **Generated:** `r Sys.time()` - **Studies:** NE20 (n=37,546), NE22 (n=2,431), NE25 (n=3,507), NSCH21 (n=1,000 sampled), NSCH22 (n=1,000 sampled), USA24 (n=1,600) For questions or to report data quality concerns, contact the Calibration Pipeline Team. :::